At least they document the changes, I don't know if libdnet ever merged those back, it might be worth looking at that.
I just had a quick look and it appears that all/most of the changes are not included in libdnet-1.11.
I don't think there is any way we can fix this currently. The modifications made in the nmap version include some fixes and a patch that adds support for SCTP. Nmap won't compile against a libdnet which doesn't have this patch, and it's not included in the upstream version (yet).
What I found out about disentangling the bundled libs so far:
1) libdnet-stripped is hard-coded in various C headers and elsewhere
2) dev-libs/libdnet-1.12 supports SCTP, so we should be able to fairly easily switch, if it
weren't for 1).
3) liblinear is not in the tree
4) autotools changes are difficult (e.g. )
I made some initial progress but then I got tired and threw away my work in disgust. This isn't going to be easy.
 CHANGELOG:Cleaned up the libpcre build system a bit by removing Makefile.am
any news about this? this seems to block nmap 6.40 which is out since 29-Jul-2013
(In reply to puchu from comment #4)
> any news about this? this seems to block nmap 6.40 which is out since
>=dev-lang/lua-5.2 is still package.masked.